Detection of chain backfolding in simulation of DNA in nanofluidic channels

Abstract

The DNA extension in cylindrical nanochannels under moderately strong confinements in the “transition” region, where experiments are conducted, is examined by Monte Carlo simulations. The focal point is estimation of the amount of backfolding structures such as hairpins and loops in extended (linearized) DNA molecules. At the chain-ends of DNA an extensive folding (mainly as the J-type hairpins) is detected under all confinements, covering the Odijk and de Gennes regimes and the transition region between them. In contrast, in the DNA chain interior, the backfolding into Z-type hairpins is abundant in the de Gennes regime, significantly reduced in the transition region, and practically absent in the Odijk regime. The linear relationship between the DNA extension and its contour length is validated also in the transition region where explicit theories are absent.